runReverseDecon {SpatialDecon} | R Documentation

## Run Reversedecon

### Description

Runs reversedecon from an S4 object

### Usage

    runReverseDecon(object, ...)

### Arguments

`object` | An S4 object such as a GeoMxSet object
`...` | Arguments passed to reversedecon

### Value

list containing modeled gene expression's ~ cell scores

### Examples

    library(GeomxTools)
    datadir <- system.file("extdata", "DSP_NGS_Example_Data", package = "GeomxTools")
    demoData <- readRDS(file.path(datadir, "/demoData.rds"))

    demoData <- shiftCountsOne(demoData)
    target_demoData <- aggregateCounts(demoData)

    target_demoData <- normalize(target_demoData, "quant")

    # run basic decon:
    res0 <- runspatialdecon(object = target_demoData,
                            norm_elt = "exprs_norm",
                            raw_elt = "exprs")

    # run reverse decon:
    target_demoData <- runReverseDecon(object = target_demoData,
                                       norm_elt = "exprs_norm",
                                       beta = pData(res0)$beta)

[Package SpatialDecon version 1.4.3 Index]